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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Sun Jun 06 2010
Journal Name
Baghdad Science Journal
Preparation of Media for Growth and Isolation of Lactic Acid Bacteria by Using the Starch-Industry by- Products
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By- products of corn starch industry were used to prepare media for propagation the lactic acid bacteria as a natural auxotroph. The by- products used were the corn steep water (S) and gluten extract (G) after a proper treatment to get them ready for media preparation. The results showed that it was possible to replace the peptone and meat extract by gluten extract in MRS medium. The growth was approximately similar to that obtained in standard MRS media. Corn steep water (S) was used as well and the growth enhanced by including Tween – 80 at 1% level. The later media named MZ, which was superior for growing standard and local strains and starters. The MZ medium modified by adding acetate and glacial acetic acid similarly to

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Publication Date
Tue Dec 31 2013
Journal Name
Al-khwarizmi Engineering Journal
Beneficiation of Iraqi Akash at Phosphate Ore Using Organic Acids for the Production of Wet Process Phosphoric Acid
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In the present work, leaching process studiedusing organic acids (acetic acid and lactic acid) to extract phosphate from the Iraqi Akashat phosphate ore by separation of calcareous materials (mainly calcite). This approach characterized by energy conservation, environmental enhancement by recovery of calcite as calcium sulfate (gypsum), keeping the physical and chemical properties of apatite. Samples were analyzed using X-ray diffraction and FTIR spectrophotometer. From the obtained experimental data it was found that using the two organic acids yields closed purity values of the produced apatite at the optimum conditions, while at different acid concentrations, it was found that the efficiency of acetic acid is higher at the low acid co

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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of Engineering
The Effective of Pressure and Sintering Temperature for Hardness Characteristics of Shape Memory Alloy by Using Taguchi Technique
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This paper presents the Taguchi approach for optimization of hardness for  shape memory alloy (Cu-Al-Ni) . The influence of  powder metallurgy parameters on hardness has been investigated. Taguchi technique and ANOVA were used for analysis. Nine experimental runs based on Taguchi’s L9 orthogonal array were performed (OA),for two parameters was study (Pressure and sintering temperature) for three different levels (300 ,500 and 700) MPa ,(700 ,800 and  900)oC respectively . Main effect, signal-to-noise (S/N) ratio was study, and analysis of variance (ANOVA) using  to investigate the micro-hardness characteristics of the shape memory alloy .after application the result of study shown the hei

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Publication Date
Sun Jan 02 2005
Journal Name
Asian Journal Of Information Technology
Simple Flight Simulator Model
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Pilots are trained using computerized flight simulators. A flight simulator is a training system where pilots can acquire flying skills without need to practice on a real airplane. Simulators are used by professional pilots to practice flying strategies under emergency or hazardous conditions, or to train on new aircraft types. In this study a framework for flight simulation is presented and the layout of an implemented program is described. The calculations were based on simple theoretical approach. The implementation was based on utilizing some of utilities supported by ActiveX, DirectX and OpenGL written in Visual C++. The main design consideration is to build a simple flight simulation program can operate without need to high computer e

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Publication Date
Thu Nov 06 2025
Journal Name
Frontiers In Oral Health
Irisin, a promising adipomyokine, shows low levels in relation to periodontal diseases, unlike visfatin and IL-6 (case-control study)
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Introduction

Adipose tissue releases pro- and anti-inflammatory cytokines and hormones such as irisin, visfatin, and interleukin-6, which may be linked to periodontal diseases.

Objectives

Our study aimed to determine salivary irisin, visfatin, and interleukin-6 levels in gingivitis and periodontitis patients, compare them with healthy periodontal patients, and evaluate the association between these biomarkers.

Materials a
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Publication Date
Thu May 29 2025
Journal Name
Bmc Public Health
Coping skills and associated sociodemographic, clinical, and psychological factors among women with breast cancer in Iraq: a cross-sectional study”
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Background: Coping skills play a vital role in managing the physical and psychological effects of breast cancer (BC). Despite improvements in early detection and treatment, Breast cancer survivors continue to face long-term challenges after diagnosis. Therefore, this study aims to evaluate the coping skills employed by breast cancer women in Iraq and to identify the sociodemographic, clinical, and psychological factors associated with these coping skills. Methods: A cross-sectional study was conducted among 244 breast cancer women in The Medical City Teaching Oncology Hospital, Baghdad, Iraq, from August 2023 to October 2023, coping skills and psychological factors were assessed using the BRIEF COPE-28, and Hospital Anxiety Depression scale

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Publication Date
Tue Oct 14 2025
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Illness Perceptions and Response to Treatment with Romiplostim in Iraqi Patients with Refractory Immune Thrombocytopenia Purpura: A Cross-Sectional Study
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Background: Immune thrombocytopenia is an immune-related disorder that causes an impairment in platelet production and stimulates platelet destruction, causing variable bleeding symptoms. Objective: This study focuses on refractory immune thrombocytopenic purpura patients on romiplostim treatment and their level of illness perception related to treatment response. Method: A cross-sectional study was conducted from May 1st, 2025, to August 1st, 2025. Brief Illness Perception Questionnaires were administered to 84 patients with ITP to collect the data. The study took place at the Hematology and Bone Marrow Transplant Center, Medical City, Baghdad, Iraq. Results: The romiplostim response rate is 21 (25.0%), while the partial response rate is 4

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Publication Date
Thu Dec 05 2024
Journal Name
Shifaa
Evaluating alveolar bone thickness in upper and lower incisors from orthodontic perspective. A Cone beam computed tomography-based retrospective study
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Purpose: This study aimed to assess the thickness of alveolar bone of maxillary and mandibular incisors from orthodontics perspective. Materials and Method: A total of 73 Cone beam computed tomography for Iraqi patients (47 females and 26 males) were included in this study. The selected images were captured and imported to AutoCAD database software to perform the measurement. To measure alveolar bone thickness, a reference line was drawn through the long axis of each incisor, from the incisal edge to the root apex. Then, labial and lingual/palatal perpendicular lines were drawn to the reference line at 3, 6, and 9mm apically from the cemento-enamel junction (CEJ). Results: The buccal bone is generally thinner than the lingual/palata

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Publication Date
Sun Apr 30 2023
Journal Name
Al-kindy College Medical Journal
The Surgical outcomes of fundus-first technique in lowering the rate of bile duct injuries and bleeding during open cholecystectomy that facing intraoperative difficulties: A single-center prospective study: The surgical outcomes of open fundus-first cholecystectomy technique.
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Background: The problem of difficult gallbladder is not clearly defined and associated with real missing of therapeutic approaches that decreased morbidity. Moreover, the difficult gallbladder was reported as a contributing risk factor for biliary injury due to raised difficulty in surgical dissection within Calot’s triangle. The aim of this study is to determine the surgical outcomes of the open fundus-first cholecystectomy in lowering the rate of lethal intraoperative risks.

Subjects and Methods: Our prospective study conducted during the period of January 2019 to December 2022 at Ibn Sina specialized hospital, Khartoum, Sudan, for two hundred and fifty-three patients underw

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Publication Date
Wed Apr 01 2009
Journal Name
International Journal Of Applied Environmental Sciences
An expert System for Predicting the Effects of Noise Pollution on Grass Trimming Task Using Fuzzy Modeling
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Grass trimming operation is widely done in Malaysia for the purpose of maintaining highways. Large number of operators engaged in this work encounters high level of noise generated by back pack type grass trimmer used for this purpose. High level of noise exposure gives different kinds of ill effect on human operators. Exact nature of deteriorated work performance is not known. For predicting the work efficiency deterioration, fuzzy tool has been used in present research. It has been established that a fuzzy computing system will help in identification and analysis of fuzzy models fuzzy system offers a convenient way of representing the relationships between the inputs and outputs of a system in the form of IF-THEN rules. The paper presents

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